3-112095870-G-A

Position:

• chr3-112095870-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024616.3(C3orf52):​c.268+2381G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 151,746 control chromosomes in the GnomAD database, including 22,956 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.53 (22956 hom., cov: 30)
• Consequence: C3orf52 NM_024616.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302

Genes affected

C3orf52 (HGNC:26255): (chromosome 3 open reading frame 52) Predicted to be located in endoplasmic reticulum membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C3orf52	NM_024616.3	c.268+2381G>A		intron_variant		ENST00000264848.10
C3orf52	NM_001171747.2	c.268+2381G>A		intron_variant
C3orf52	XR_007095726.1	n.287+2381G>A		intron_variant, non_coding_transcript_variant
C3orf52	XR_924171.4	n.287+2381G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C3orf52	ENST00000264848.10	c.268+2381G>A		intron_variant		1	NM_024616.3	P1

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80235 AN: 151630 Hom.: 22948 Cov.: 30

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.548

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.529 AC: 80265 AN: 151746 Hom.: 22956 Cov.: 30 AF XY: 0.535 AC XY: 39643 AN XY: 74164

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.598

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.552

Alfa AF: 0.592 Hom.: 12131

Bravo AF: 0.519

Asia WGS AF: 0.644 AC: 2242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.58

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4682357; hg19: chr3-111814717;